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Vanni C, Schechter MS, Acinas SG, Barberán A, Buttigieg PL, Casamayor EO, Delmont TO, Duarte CM, Eren AM, Finn RD, Kottmann R, Mitchell A, Sánchez P, Siren K, Steinegger M, Gloeckner FO, Fernàndez-Guerra A. Unifying the known and unknown microbial coding sequence space. eLife 2022; 11:67667. [PMID: 35356891 PMCID: PMC9132574 DOI: 10.7554/elife.67667] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40–60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we present a conceptual framework, its translation into the computational workflow AGNOSTOS and a demonstration on how we can bridge the known-unknown gap in genomes and metagenomes. By analyzing 415,971,742 genes predicted from 1749 metagenomes and 28,941 bacterial and archaeal genomes, we quantify the extent of the unknown fraction, its diversity, and its relevance across multiple organisms and environments. The unknown sequence space is exceptionally diverse, phylogenetically more conserved than the known fraction and predominantly taxonomically restricted at the species level. From the 71 M genes identified to be of unknown function, we compiled a collection of 283,874 lineage-specific genes of unknown function for Cand. Patescibacteria (also known as Candidate Phyla Radiation, CPR), which provides a significant resource to expand our understanding of their unusual biology. Finally, by identifying a target gene of unknown function for antibiotic resistance, we demonstrate how we can enable the generation of hypotheses that can be used to augment experimental data. It is estimated that scientists do not know what half of microbial genes actually do. When these genes are discovered in microorganisms grown in the lab or found in environmental samples, it is not possible to identify what their roles are. Many of these genes are excluded from further analyses for these reasons, meaning that the study of microbial genes tends to be limited to genes that have already been described. These limitations hinder research into microbiology, because information from newly discovered genes cannot be integrated to better understand how these organisms work. Experiments to understand what role these genes have in the microorganisms are labor-intensive, so new analytical strategies are needed. To do this, Vanni et al. developed a new framework to categorize genes with unknown roles, and a computational workflow to integrate them into traditional analyses. When this approach was applied to over 400 million microbial genes (both with known and unknown roles), it showed that the share of genes with unknown functions is only about 30 per cent, smaller than previously thought. The analysis also showed that these genes are very diverse, revealing a huge space for future research and potential applications. Combining their approach with experimental data, Vanni et al. were able to identify a gene with a previously unknown purpose that could be involved in antibiotic resistance. This system could be useful for other scientists studying microorganisms to get a more complete view of microbial systems. In future, it may also be used to analyze the genetics of other organisms, such as plants and animals.
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Affiliation(s)
- Chiara Vanni
- Microbial Genomics and Bioinformatics Research G, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar-CMIMA (CSIC), Barcelona, Spain
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, United States
| | - Pier Luigi Buttigieg
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Bremerhaven, Germany
| | - Emilio O Casamayor
- Center for Advanced Studies of Blanes CEAB-CSIC, Spanish Council for Research, Blanes, Spain
| | - Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Paris, France
| | - Carlos M Duarte
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, United States
| | - Robert D Finn
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, United Kingdom
| | - Renzo Kottmann
- Microbial Genomics and Bioinformatics Research G, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Alex Mitchell
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, United Kingdom
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar-CMIMA (CSIC), Barcelona, Spain
| | - Kimmo Siren
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Frank Oliver Gloeckner
- MARUM, Helmholtz Center for Polar and Marine Research, University of Bremen, Bremen, Germany
| | - Antonio Fernàndez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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Alfreider A, Tartarotti B. Spatiotemporal dynamics of different CO 2 fixation strategies used by prokaryotes in a dimictic lake. Sci Rep 2019; 9:15068. [PMID: 31636358 PMCID: PMC6803681 DOI: 10.1038/s41598-019-51584-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/30/2019] [Indexed: 01/18/2023] Open
Abstract
The Calvin-Benson-Bassham (CBB) cycle and the 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle are two inorganic carbon assimilation pathways widely used by prokaryotic autotrophs in lakes. We investigated the effect of mixing periods and stable water stratification patterns on the trajectories of both CO2 fixation strategies in a dimictic lake (Piburger See), because information on the spatiotemporal dynamics of prokaryotes using these pathways in freshwater ecosystems is far from complete. Based on a quantitative approach (droplet digital PCR) of genes coding for key enzymes in different CO2 assimilation pathways, nine depths covering the entire water column were investigated on a monthly basis for one year. Our data show that the abundance of photoautotrophs and obligate chemolithoautotrophs preferentially using form IA RubisCO was determined by seasonal variations. Highest numbers were observed in summer, while a strong decline of prokrayotes using RubisCO form IA was measured between December and May, the period where the lake was mostly covered by ice. The spatiotemporal distribution patterns of genes coding for RubisCO form IC genes, an enzyme usually used by facultative autotrophs for CO2 assimilation, were less pronounced. Bacteria harboring RubisCO form II were dominating the oxygen limited hypolimnion, while nitrifying Thaumarchaeota using the HP/HB cycle were of minor importance in the lake. Our data reveal that the seasonal heterogeneity, which is determined by the dimictic thermal regime of the lake, results in pronounced spatiotemporal changes of different CO2 assimilation pathways with depth-dependent environmental parameters as key factors for their distribution.
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Affiliation(s)
- Albin Alfreider
- Department of Ecology, University of Innsbruck, Innsbruck, Austria.
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Alfreider A, Grimus V, Luger M, Ekblad A, Salcher MM, Summerer M. Autotrophic carbon fixation strategies used by nitrifying prokaryotes in freshwater lakes. FEMS Microbiol Ecol 2019; 94:5076030. [PMID: 30137292 PMCID: PMC6118323 DOI: 10.1093/femsec/fiy163] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 12/02/2022] Open
Abstract
Niche specialization of nitrifying prokaryotes is usually studied with tools targeting molecules involved in the oxidation of ammonia and nitrite. The ecological significance of diverse CO2 fixation strategies used by nitrifiers is, however, mostly unexplored. By analyzing autotrophy-related genes in combination with amoA marker genes based on droplet digitial PCR and CARD-FISH counts targeting rRNA, we quantified the distribution of nitrifiers in eight stratified lakes. Ammonia oxidizing (AO) Thaumarchaeota using the 3-hydroxypropionate/4-hydroxybutyrate pathway dominated deep and oligotrophic lakes, whereas Nitrosomonas-related taxa employing the Calvin cycle were important AO bacteria in smaller lakes. The occurrence of nitrite oxidizing Nitrospira, assimilating CO2 with the reductive TCA cycle, was strongly correlated with the distribution of Thaumarchaeota. Recently discovered complete ammonia-oxidizing bacteria (comammox) belonging to Nitrospira accounted only for a very small fraction of ammonia oxidizers (AOs) present at the study sites. Altogether, this study gives a first insight on how physicochemical characteristics in lakes are associated to the distribution of nitrifying prokaryotes with different CO2 fixation strategies. Our investigations also evaluate the suitability of functional genes associated with individual CO2 assimilation pathways to study niche preferences of different guilds of nitrifying microorganisms based on an autotrophic perspective.
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Affiliation(s)
- Albin Alfreider
- Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Victoria Grimus
- Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Martin Luger
- Institute for Water Ecology, Fisheries Biology and Lake Research, Federal Agency for Water Management, Scharfling 18, 5310 Mondsee, Austria
| | - Anja Ekblad
- Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách, 702/7370 05 Ceské Budejovice, Czech Republic
| | - Monika Summerer
- Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
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Abstract
Lake Faro, in the North-Eastern corner of Sicily (Italy), shows the typical stratification of a meromictic tempered basin, with a clear identification of the mixolimnion and the monimolimnion, separated by an interfacial chemocline. In this study, an annual-scaled study on the space-time distribution of the microbial communities in water samples of Lake Faro was performed by both ARISA (Amplified Ribosomal Intergenic Spacer Analysis) and CARD-FISH (Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization) approaches. A correlation between microbial parameters and both environmental variables (i.e., temperature, pH, dissolved oxygen, redox potential, salinity, chlorophyll-a) and mixing conditions was highlighted, with an evident seasonal variability. The most significative differences were detected by ARISA between the mixolimnion and the monimolimnion, and between Spring and Autumn, by considering layer and season as a factor, respectively.
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La Cono V, Ruggeri G, Azzaro M, Crisafi F, Decembrini F, Denaro R, La Spada G, Maimone G, Monticelli LS, Smedile F, Giuliano L, Yakimov MM. Contribution of Bicarbonate Assimilation to Carbon Pool Dynamics in the Deep Mediterranean Sea and Cultivation of Actively Nitrifying and CO 2-Fixing Bathypelagic Prokaryotic Consortia. Front Microbiol 2018; 9:3. [PMID: 29403458 PMCID: PMC5780414 DOI: 10.3389/fmicb.2018.00003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/03/2018] [Indexed: 11/16/2022] Open
Abstract
Covering two-thirds of our planet, the global deep ocean plays a central role in supporting life on Earth. Among other processes, this biggest ecosystem buffers the rise of atmospheric CO2. Despite carbon sequestration in the deep ocean has been known for a long time, microbial activity in the meso- and bathypelagic realm via the "assimilation of bicarbonate in the dark" (ABD) has only recently been described in more details. Based on recent findings, this process seems primarily the result of chemosynthetic and anaplerotic reactions driven by different groups of deep-sea prokaryoplankton. We quantified bicarbonate assimilation in relation to total prokaryotic abundance, prokaryotic heterotrophic production and respiration in the meso- and bathypelagic Mediterranean Sea. The measured ABD values, ranging from 133 to 370 μg C m-3 d-1, were among the highest ones reported worldwide for similar depths, likely due to the elevated temperature of the deep Mediterranean Sea (13-14°C also at abyssal depths). Integrated over the dark water column (≥200 m depth), bicarbonate assimilation in the deep-sea ranged from 396 to 873 mg C m-2 d-1. This quantity of produced de novo organic carbon amounts to about 85-424% of the phytoplankton primary production and covers up to 62% of deep-sea prokaryotic total carbon demand. Hence, the ABD process in the meso- and bathypelagic Mediterranean Sea might substantially contribute to the inorganic and organic pool and significantly sustain the deep-sea microbial food web. To elucidate the ABD key-players, we established three actively nitrifying and CO2-fixing prokaryotic enrichments. Consortia were characterized by the co-occurrence of chemolithoautotrophic Thaumarchaeota and chemoheterotrophic proteobacteria. One of the enrichments, originated from Ionian bathypelagic waters (3,000 m depth) and supplemented with low concentrations of ammonia, was dominated by the Thaumarchaeota "low-ammonia-concentration" deep-sea ecotype, an enigmatic and ecologically important group of organisms, uncultured until this study.
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Affiliation(s)
- Violetta La Cono
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Gioachino Ruggeri
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Maurizio Azzaro
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Francesca Crisafi
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Franco Decembrini
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Renata Denaro
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Gina La Spada
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Giovanna Maimone
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Luis S. Monticelli
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Francesco Smedile
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Laura Giuliano
- Mediterranean Science Commission (CIESM), Monaco, Monaco
| | - Michail M. Yakimov
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
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6
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Bortoluzzi G, Romeo T, La Cono V, La Spada G, Smedile F, Esposito V, Sabatino G, Di Bella M, Canese S, Scotti G, Bo M, Giuliano L, Jones D, Golyshin PN, Yakimov MM, Andaloro F. Ferrous iron- and ammonium-rich diffuse vents support habitat-specific communities in a shallow hydrothermal field off the Basiluzzo Islet (Aeolian Volcanic Archipelago). GEOBIOLOGY 2017; 15:664-677. [PMID: 28383164 DOI: 10.1111/gbi.12237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 03/09/2017] [Indexed: 06/07/2023]
Abstract
Ammonium- and Fe(II)-rich fluid flows, known from deep-sea hydrothermal systems, have been extensively studied in the last decades and are considered as sites with high microbial diversity and activity. Their shallow-submarine counterparts, despite their easier accessibility, have so far been under-investigated, and as a consequence, much less is known about microbial communities inhabiting these ecosystems. A field of shallow expulsion of hydrothermal fluids has been discovered at depths of 170-400 meters off the base of the Basiluzzo Islet (Aeolian Volcanic Archipelago, Southern Tyrrhenian Sea). This area consists predominantly of both actively diffusing and inactive 1-3 meters-high structures in the form of vertical pinnacles, steeples and mounds covered by a thick orange to brown crust deposits hosting rich benthic fauna. Integrated morphological, mineralogical, and geochemical analyses revealed that, above all, these crusts are formed by ferrihydrite-type Fe3+ oxyhydroxides. Two cruises in 2013 allowed us to monitor and sampled this novel ecosystem, certainly interesting in terms of shallow-water iron-rich site. The main objective of this work was to characterize the composition of extant communities of iron microbial mats in relation to the environmental setting and the observed patterns of macrofaunal colonization. We demonstrated that iron-rich deposits contain complex and stratified microbial communities with a high proportion of prokaryotes akin to ammonium- and iron-oxidizing chemoautotrophs, belonging to Thaumarchaeota, Nitrospira, and Zetaproteobacteria. Colonizers of iron-rich mounds, while composed of the common macrobenthic grazers, predators, filter-feeders, and tube-dwellers with no representatives of vent endemic fauna, differed from the surrounding populations. Thus, it is very likely that reduced electron donors (Fe2+ and NH4+ ) are important energy sources in supporting primary production in microbial mats, which form a habitat-specific trophic base of the whole Basiluzzo hydrothermal ecosystem, including macrobenthic fauna.
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Affiliation(s)
- G Bortoluzzi
- Institute for Marine Sciences, ISMAR-CNR, Bologna, Italy
| | - T Romeo
- Institute for Environmental Protection and Research, ISPRA, Milazzo, Italy
| | - V La Cono
- Institute for Coastal Marine Environment, IAMC-CNR, Messina, Italy
| | - G La Spada
- Institute for Coastal Marine Environment, IAMC-CNR, Messina, Italy
| | - F Smedile
- Institute for Coastal Marine Environment, IAMC-CNR, Messina, Italy
| | - V Esposito
- Institute for Environmental Protection and Research, ISPRA, Milazzo, Italy
| | - G Sabatino
- Department of Physics and Earth Sciences, University of Messina, Messina, Italy
| | - M Di Bella
- National Institute of Geophysics and Volcanology, Palermo, Italy
| | - S Canese
- Institute for Environmental Protection and Research, ISPRA, Milazzo, Italy
| | - G Scotti
- Institute for Environmental Protection and Research, ISPRA, Milazzo, Italy
| | - M Bo
- DISTAV, University of Genoa, Genoa, Italy
| | - L Giuliano
- Institute for Coastal Marine Environment, IAMC-CNR, Messina, Italy
| | - D Jones
- School of Environment, Natural Resources & Geography, Bangor University, Bangor, UK
| | - P N Golyshin
- School of Biological Sciences, Bangor University, Bangor, UK
- Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - M M Yakimov
- Institute for Coastal Marine Environment, IAMC-CNR, Messina, Italy
- Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - F Andaloro
- Institute for Environmental Protection and Research, ISPRA, Palermo, Italy
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Alfreider A, Baumer A, Bogensperger T, Posch T, Salcher MM, Summerer M. CO 2 assimilation strategies in stratified lakes: Diversity and distribution patterns of chemolithoautotrophs. Environ Microbiol 2017; 19:2754-2768. [PMID: 28474482 PMCID: PMC5619642 DOI: 10.1111/1462-2920.13786] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 11/23/2022]
Abstract
While mechanisms of different carbon dioxide (CO2) assimilation pathways in chemolithoautotrohic prokaryotes are well understood for many isolates under laboratory conditions, the ecological significance of diverse CO2 fixation strategies in the environment is mostly unexplored. Six stratified freshwater lakes were chosen to study the distribution and diversity of the Calvin-Benson-Bassham (CBB) cycle, the reductive tricarboxylic acid (rTCA) cycle, and the recently discovered archaeal 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) pathway. Eleven primer sets were used to amplify and sequence genes coding for selected key enzymes in the three pathways. Whereas the CBB pathway with different forms of RubisCO (IA, IC and II) was ubiquitous and related to diverse bacterial taxa, encompassing a wide range of potential physiologies, the rTCA cycle in Epsilonproteobacteria and Chloribi was exclusively detected in anoxic water layers. Nitrifiying Nitrosospira and Thaumarchaeota, using the rTCA and HP/HB cycle respectively, are important residents in the aphotic and (micro-)oxic zone of deep lakes. Both taxa were of minor importance in surface waters and in smaller lakes characterized by an anoxic hypolimnion. Overall, this study provides a first insight on how different CO2 fixation strategies and chemical gradients in lakes are associated to the distribution of chemoautotrophic prokaryotes with different functional traits.
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Affiliation(s)
- Albin Alfreider
- Institute for Ecology, University of Innsbruck, Innsbruck, Austria
| | - Andreas Baumer
- Institute for Ecology, University of Innsbruck, Innsbruck, Austria
| | | | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Michaela M Salcher
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland.,Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Monika Summerer
- Institute for Ecology, University of Innsbruck, Innsbruck, Austria
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GDGT distribution in a stratified lake and implications for the application of TEX 86 in paleoenvironmental reconstructions. Sci Rep 2016; 6:34465. [PMID: 27694918 PMCID: PMC5046090 DOI: 10.1038/srep34465] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 09/13/2016] [Indexed: 11/08/2022] Open
Abstract
We investigated the relationship between distributions of GDGTs, GDGT-based proxies and environmental factors in a stratified lake in northwestern Norway. More than 90% of isoGDGTs were produced at the bottom of the oxycline, indicating a predominance of ammonia-oxidizing Group I.1a of Thaumarchaeota, supported by high crenarchaeol/caldarchaeol ratios. Dissolved oxygen content, rather than temperature, exercised a primary control on TEX86 values. In spite of low BIT value in surface sediment, the reconstructed lake surface temperature was "cold" biased. MBT values in streams and lake surface water were significantly smaller than those in the catchment soil, suggesting in situ production of brGDGTs in streams. A rapid transition of MBT vs. temperature/pH relationships occurring at the bottom of oxycline indicated the differential production of various brGDGTs with D.O. and depths. Only within the oxycline were CBT-based pH values close to in situ pH. Our results confirm earlier studies calling for caution in applying TEX86 as a surface temperature proxy, or MBT and/or CBT for reconstructing pH, in anoxic or euxinic lakes, estuaries and ocean basins. We propose that caldarchaeol/crenarchaeol ratio, an indicator of contributions from methanogenic archaea, together with the BIT and TEX86 proxies, can help reconstruct past levels of stratification.
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Jessen GL, Lichtschlag A, Struck U, Boetius A. Distribution and Composition of Thiotrophic Mats in the Hypoxic Zone of the Black Sea (150-170 m Water Depth, Crimea Margin). Front Microbiol 2016; 7:1011. [PMID: 27446049 PMCID: PMC4925705 DOI: 10.3389/fmicb.2016.01011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/14/2016] [Indexed: 01/28/2023] Open
Abstract
At the Black Sea chemocline, oxygen- and sulfide-rich waters meet and form a niche for thiotrophic pelagic bacteria. Here we investigated an area of the Northwestern Black Sea off Crimea close to the shelf break, where the chemocline reaches the seafloor at around 150-170 m water depth, to assess whether thiotrophic bacteria are favored in this zone. Seafloor video transects were carried out with the submersible JAGO covering 20 km(2) on the region between 110 and 200 m depth. Around the chemocline we observed irregular seafloor depressions, covered with whitish mats of large filamentous bacteria. These comprised 25-55% of the seafloor, forming a belt of 3 km width around the chemocline. Cores from the mats obtained with JAGO showed higher accumulations of organic matter under the mats compared to mat-free sediments. The mat-forming bacteria were related to Beggiatoa-like large filamentous sulfur bacteria based on 16S rRNA sequences from the mat, and visual characteristics. The microbial community under the mats was significantly different from the surrounding sediments and enriched with taxa affiliated with polymer degrading, fermenting and sulfate reducing microorganisms. Under the mats, higher organic matter accumulation, as well as higher remineralization and radiotracer-based sulfate reduction rates were measured compared to outside the mat. Mat-covered and mat-free sediments showed similar degradability of the bulk organic matter pool, suggesting that the higher sulfide fluxes and subsequent development of the thiotrophic mats in the patches are consequences of the accumulation of organic matter rather than its qualitative composition. Our observations suggest that the key factors for the distribution of thiotrophic mat-forming communities near to the Crimean shelf break are hypoxic conditions that (i) repress grazers, (ii) enhance the accumulation and degradation of labile organic matter by sulfate-reducers, and (iii) favor thiotrophic filamentous bacteria which are adapted to exploit steep gradients in oxygen and sulfide availability; in addition to a specific seafloor topography which may relate to internal waves at the shelf break.
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Affiliation(s)
- Gerdhard L Jessen
- HGF-MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Anna Lichtschlag
- HGF-MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Ulrich Struck
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung Berlin, Germany
| | - Antje Boetius
- HGF-MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany; Alfred Wegener Institute, Helmholtz Center for Polar and Marine ResearchBremerhaven, Germany
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10
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La Cono V, Smedile F, La Spada G, Arcadi E, Genovese M, Ruggeri G, Genovese L, Giuliano L, Yakimov MM. Shifts in the meso- and bathypelagic archaea communities composition during recovery and short-term handling of decompressed deep-sea samples. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:450-459. [PMID: 25682761 DOI: 10.1111/1758-2229.12272] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 02/10/2015] [Indexed: 06/04/2023]
Abstract
Dark ocean microbial communities are actively involved in chemoautotrophic and anaplerotic fixation of bicarbonate. Thus, aphotic pelagic realm of the ocean might represent a significant sink of CO2 and source of primary production. However, the estimated metabolic activities in the dark ocean are fraught with uncertainties. Typically, deep-sea samples are recovered to the sea surface for downstream processing on deck. Shifts in ambient settings, associated with such treatments, can likely change the metabolic activity and community structure of deep-sea adapted autochthonous microbial populations. To estimate influence of recovery and short-term handling of deep-sea samples, we monitored the succession of bathypelagic microbial community during its 3 days long on deck incubation. We demonstrated that at the end of exposition, the deep-sea archaeal population decreased threefold, whereas the bacterial fraction doubled in size. As revealed by phylogenetic analyses of amoA gene transcripts, dominance of the active ammonium-oxidizing bathypelagic Thaumarchaeota groups shifted over time very fast. These findings demonstrated the simultaneous existence of various 'deep-sea ecotypes', differentially reacting to the sampling and downstream handling. Our study supports the hypothesis that metabolically active members of meso- and bathypelagic Thaumarchaeota possess the habitat-specific distribution, metabolic complexity and genetic divergence at subpopulation level.
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Affiliation(s)
- Violetta La Cono
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Francesco Smedile
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Gina La Spada
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Erika Arcadi
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Maria Genovese
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Gioacchino Ruggeri
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Lucrezia Genovese
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Laura Giuliano
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
- Mediterranean Science Commission (CIESM), 16 bd de Suisse, Monte Carlo, 98000, Monaco
| | - Michail M Yakimov
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
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Gutiérrez MH, Galand PE, Moffat C, Pantoja S. Melting glacier impacts community structure of Bacteria, Archaea and Fungi in a Chilean Patagonia fjord. Environ Microbiol 2015; 17:3882-97. [PMID: 25856307 DOI: 10.1111/1462-2920.12872] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 04/02/2015] [Accepted: 04/02/2015] [Indexed: 01/30/2023]
Abstract
Jorge Montt glacier, located in the Patagonian Ice Fields, has undergone an unprecedented retreat during the past century. To study the impact of the meltwater discharge on the microbial community of the downstream fjord, we targeted Bacteria, Archaea and Fungi communities during austral autumn and winter. Our results showed a singular microbial community present in cold and low salinity surface waters during autumn, when a thicker meltwater layer was observed. Meltwater bacterial sequences were related to Cyanobacteria, Proteobacteria, Actinobacteria and Bacteriodetes previously identified in freshwater and cold ecosystems, suggesting the occurrence of microorganisms adapted to live in the extreme conditions of meltwater. For Fungi, representative sequences related to terrestrial and airborne fungal taxa indicated transport of allochthonous Fungi by the meltwater discharge. In contrast, bottom fjord waters from autumn and winter showed representative Operational Taxonomic Units (OTUs) related to sequences of marine microorganisms, which is consistent with current models of fjord circulation. We conclude that meltwater can significantly modify the structure of microbial communities and support the development of a major fraction of microorganisms in surface waters of Patagonian fjords.
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Affiliation(s)
- Marcelo H Gutiérrez
- Department of Oceanography, Universidad de Concepción, Concepción, Chile.,COPAS Sur-Austral Program, Universidad de Concepción, Concepción, Chile
| | - Pierre E Galand
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, F-66650, Banyuls sur Mer, France
| | - Carlos Moffat
- Department of Oceanography, Universidad de Concepción, Concepción, Chile.,COPAS Sur-Austral Program, Universidad de Concepción, Concepción, Chile.,Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Silvio Pantoja
- Department of Oceanography, Universidad de Concepción, Concepción, Chile.,COPAS Sur-Austral Program, Universidad de Concepción, Concepción, Chile
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12
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Andrei AŞ, Robeson MS, Baricz A, Coman C, Muntean V, Ionescu A, Etiope G, Alexe M, Sicora CI, Podar M, Banciu HL. Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes. ISME JOURNAL 2015; 9:2642-56. [PMID: 25932617 DOI: 10.1038/ismej.2015.60] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 02/14/2015] [Accepted: 03/18/2015] [Indexed: 11/09/2022]
Abstract
Hypersaline meromictic lakes are extreme environments in which water stratification is associated with powerful physicochemical gradients and high salt concentrations. Furthermore, their physical stability coupled with vertical water column partitioning makes them important research model systems in microbial niche differentiation and biogeochemical cycling. Here, we compare the prokaryotic assemblages from Ursu and Fara Fund hypersaline meromictic lakes (Transylvanian Basin, Romania) in relation to their limnological factors and infer their role in elemental cycling by matching taxa to known taxon-specific biogeochemical functions. To assess the composition and structure of prokaryotic communities and the environmental factors that structure them, deep-coverage small subunit (SSU) ribosomal RNA (rDNA) amplicon sequencing, community domain-specific quantitative PCR and physicochemical analyses were performed on samples collected along depth profiles. The analyses showed that the lakes harbored multiple and diverse prokaryotic communities whose distribution mirrored the water stratification patterns. Ursu Lake was found to be dominated by Bacteria and to have a greater prokaryotic diversity than Fara Fund Lake that harbored an increased cell density and was populated mostly by Archaea within oxic strata. In spite of their contrasting diversity, the microbial populations indigenous to each lake pointed to similar physiological functions within carbon degradation and sulfate reduction. Furthermore, the taxonomy results coupled with methane detection and its stable C isotope composition indicated the presence of a yet-undescribed methanogenic group in the lakes' hypersaline monimolimnion. In addition, ultrasmall uncultivated archaeal lineages were detected in the chemocline of Fara Fund Lake, where the recently proposed Nanohaloarchaeota phylum was found to thrive.
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Affiliation(s)
- Adrian-Ştefan Andrei
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babeş-Bolyai University, Cluj-Napoca, Romania.,Department of Molecular Biology and Biotechnology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Michael S Robeson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, CO, USA
| | - Andreea Baricz
- Department of Molecular Biology and Biotechnology, Babeş-Bolyai University, Cluj-Napoca, Romania.,National Institute of Research and Development for Biological Sciences (NIRDBS), Institute of Biological Research, Cluj-Napoca, Romania
| | - Cristian Coman
- Department of Molecular Biology and Biotechnology, Babeş-Bolyai University, Cluj-Napoca, Romania.,National Institute of Research and Development for Biological Sciences (NIRDBS), Institute of Biological Research, Cluj-Napoca, Romania
| | - Vasile Muntean
- Department of Molecular Biology and Biotechnology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Artur Ionescu
- Faculty of Environmental Science and Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Giuseppe Etiope
- Faculty of Environmental Science and Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania.,Istituto Nazionale di Geofisica e Vulcanologia, Rome, Italy
| | - Mircea Alexe
- Faculty of Geography, Babeş-Bolyai University, Cluj-Napoca, Romania
| | | | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Horia Leonard Banciu
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babeş-Bolyai University, Cluj-Napoca, Romania.,Department of Molecular Biology and Biotechnology, Babeş-Bolyai University, Cluj-Napoca, Romania
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13
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Hugoni M, Domaizon I, Taib N, Biderre-Petit C, Agogué H, Galand PE, Debroas D, Mary I. Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:321-329. [PMID: 25472601 DOI: 10.1111/1758-2229.12251] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 11/14/2014] [Accepted: 11/17/2014] [Indexed: 06/04/2023]
Abstract
Deep lakes are of specific interest in the study of archaeal assemblages as chemical stratification in the water column allows niche differentiation and distinct community structure. Active archaeal community and potential nitrifiers were investigated monthly over 1 year by pyrosequencing 16S rRNA transcripts and genes, and by quantification of archaeal amoA genes in two deep lakes. Our results showed that the active archaeal community patterns of spatial and temporal distribution were different between these lakes. The meromictic lake characterized by a stable redox gradient but variability in nutrient concentrations exhibited large temporal rearrangements of the dominant euryarchaeal phylotypes, suggesting a variety of ecological niches and dynamic archaeal communities in the hypolimnion of this lake. Conversely, Thaumarchaeota Marine Group I (MGI) largely dominated in the second lake where deeper water layers exhibited only short periods of complete anoxia and constant low ammonia concentrations. Investigations conducted on archaeal amoA transcripts abundance suggested that not all lacustrine Thaumarchaeota conduct the process of nitrification. A high number of 16S rRNA transcripts associated to crenarchaeal group C3 or the Miscellaneous Euryarchaeotic Group indicates the potential for these uncharacterized groups to contribute to nutrient cycling in lakes.
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Affiliation(s)
- Mylène Hugoni
- Laboratoire 'Microorganismes: Génome et Environnement', Clermont Université, Université Blaise Pascal, BP 10448, Clermont-Ferrand, F-63000, France; UMR 6023, LMGE, CNRS, Aubière, F-63171, France
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14
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Yakimov MM, La Cono V, Smedile F, Crisafi F, Arcadi E, Leonardi M, Decembrini F, Catalfamo M, Bargiela R, Ferrer M, Golyshin PN, Giuliano L. Heterotrophic bicarbonate assimilation is the main process of de novo organic carbon synthesis in hadal zone of the Hellenic Trench, the deepest part of Mediterranean Sea. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:709-722. [PMID: 25756124 DOI: 10.1111/1758-2229.12192] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ammonium-oxidizing chemoautotrophic members of Thaumarchaea are proposed to be the key players in the assimilation of bicarbonate in the dark (ABD). However, this process may also involve heterotrophic metabolic pathways, such as fixation of carbon dioxide (CO2) via various anaplerotic reactions. We collected samples from the depth of 4900 m at the Matapan-Vavilov Deep (MVD) station (Hellenic Trench, Eastern Mediterranean) and used the multiphasic approach to study the ABD mediators in this deep-sea ecosystem. At this depth, our analysis indicated the occurrence of actively CO2-fixing heterotrophic microbial assemblages dominated by Gammaproteobacteria with virtually no Thaumarchaea present. [14C]-bicarbonate incorporation experiments combined with shotgun [14C]-proteomic analysis identified a series of proteins of gammaproteobacterial origin. More than quarter of them were closely related with Alteromonas macleodii ‘deep ecotype’ AltDE, the predominant organism in the microbial community of MVD. The present study demonstrated that in the aphotic/hadal zone of the Mediterranean Sea, the assimilation of bicarbonate is associated with both chemolithoauto- and heterotrophic ABD. In some deep-sea areas, the latter may predominantly contribute to the de novo synthesis of organic carbon which points at the important and yet underestimated role heterotrophic bacterial populations can play the in global carbon cycle/sink in the ocean interior.
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Snow surface microbiome on the High Antarctic Plateau (DOME C). PLoS One 2014; 9:e104505. [PMID: 25101779 PMCID: PMC4125213 DOI: 10.1371/journal.pone.0104505] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/14/2014] [Indexed: 12/22/2022] Open
Abstract
The cryosphere is an integral part of the global climate system and one of the major habitable ecosystems of Earth's biosphere. These permanently frozen environments harbor diverse, viable and metabolically active microbial populations that represent almost all the major phylogenetic groups. In this study, we investigated the microbial diversity in the surface snow surrounding the Concordia Research Station on the High Antarctic Plateau through a polyphasic approach, including direct prokaryotic quantification by flow cytometry and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and phylogenetic identification by 16S RNA gene clone library sequencing and 454 16S amplicon pyrosequencing. Although the microbial abundance was low (<103 cells/ml of snowmelt), concordant results were obtained with the different techniques. The microbial community was mainly composed of members of the Alpha-proteobacteria class (e.g. Kiloniellaceae and Rhodobacteraceae), which is one of the most well-represented bacterial groups in marine habitats, Bacteroidetes (e.g. Cryomorphaceae and Flavobacteriaceae) and Cyanobacteria. Based on our results, polar microorganisms could not only be considered as deposited airborne particles, but as an active component of the snowpack ecology of the High Antarctic Plateau.
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Baricz A, Coman C, Andrei AS, Muntean V, Keresztes ZG, Păuşan M, Alexe M, Banciu HL. Spatial and temporal distribution of archaeal diversity in meromictic, hypersaline Ocnei Lake (Transylvanian Basin, Romania). Extremophiles 2014; 18:399-413. [PMID: 24414798 DOI: 10.1007/s00792-013-0625-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/29/2013] [Indexed: 12/31/2022]
Abstract
Saline, meromictic lakes with significant depth are usually formed as a result of salt mining activity. Ocnei Lake is one of the largest Transylvanian (Central Romania) neutral, hypersaline lake of man-made origin. We aimed to survey the seasonal dynamics of archaeal diversity in the water column of Ocnei Lake by employing microbiological methods as well as molecular techniques based on the sequence analysis of the 16S rRNA gene. We found that archaeal diversity in the water column increased with depth and salinity, with 8 OTUs being detected in the epilimnion compared to 21 found in the chemocline, and 32 OTUs in the monimolimnion. Down to 3.5 m depth, the archaeal community was markedly dominated by the presence of an unclassified archaeon sharing 93% sequence identity to Halogeometricum spp. At the chemocline, the shift in archaeal community composition was associated with an increase in salinity, the main factor affecting the vertical distribution of archaeal assemblages. It appears that the microoxic and hypersaline monimolimnion is populated by several major haloarchaeal taxa, with minor fluctuations in their relative abundances throughout all seasons. The culturable diversity was reasonably correlated to the dominant OTUs obtained by molecular methods. Our results indicate that Ocnei Lake represents a relatively stable extreme habitat, accommodating a diverse and putatively novel archaeal community, as 30% of OTUs could not be classified at the genus level.
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Affiliation(s)
- Andreea Baricz
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 5-7 Clinicilor Street, 400006, Cluj-Napoca, Romania
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